Contacts of the helix formed by residues 1198 - 1210 (chain W) in PDB entry 5IJO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU1198 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1157W ILE* 6.3 2.7 - - + -
1160W THR* 5.8 8.5 - - - -
1192W PHE 5.8 0.2 - - - -
1193W ALA* 2.8 22.3 + - - +
1196W PHE* 3.0 10.0 + - + +
1197W LYS* 1.3 71.7 - - - +
1199W ALA* 1.3 63.8 + - - +
1200W GLU* 3.3 2.2 - - + +
1201W CYS* 3.7 20.6 - - + +
1202W LYS* 3.1 19.9 + - - +
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Residues in contact with ALA1199 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197W LYS 3.0 11.1 + - - +
1198W LEU* 1.3 69.7 - - - +
1200W GLU* 1.3 66.1 + - - +
1202W LYS* 3.2 7.5 + - - +
1203W LEU* 2.9 23.6 + - - +
1220W LEU* 4.6 11.6 - - + +
1223W ASP* 5.1 4.7 - - + -
1224W ILE* 3.7 36.6 - - + +
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Residues in contact with GLU1200 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198W LEU* 3.3 1.7 - - + +
1199W ALA* 1.3 77.8 - - - +
1201W CYS* 1.3 63.5 + - - +
1203W LEU* 3.1 8.9 + - - +
1204W ALA* 2.9 23.0 + - - +
1224W ILE* 5.5 0.4 - - - +
1251W LEU* 4.9 18.9 - - + +
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Residues in contact with CYS1201 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153W ILE* 5.9 4.0 - - + +
1156W GLN* 5.9 4.9 - - + -
1157W ILE* 5.5 14.8 - - + +
1193W ALA* 4.9 5.4 - - + -
1198W LEU* 3.5 22.8 + - + +
1199W ALA 3.2 0.2 - - - -
1200W GLU* 1.3 78.3 - - - +
1202W LYS* 1.3 64.5 + - - +
1204W ALA* 3.0 8.6 + - - +
1205W ILE* 2.8 25.0 + - - +
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Residues in contact with LYS1202 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189W TYR* 6.0 2.9 - - + +
1193W ALA* 3.8 18.8 - - + +
1198W LEU 3.1 12.6 + - - +
1199W ALA* 3.4 12.6 - - - +
1201W CYS* 1.3 78.8 - - - +
1203W LEU* 1.3 62.0 + - - +
1205W ILE* 3.2 8.0 + - - +
1206W ILE* 3.0 23.9 + - - +
1220W LEU* 5.7 7.6 - - + -
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Residues in contact with LEU1203 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199W ALA 2.9 13.2 + - - +
1200W GLU* 3.1 11.4 + - - +
1202W LYS* 1.3 76.7 - - - +
1204W ALA* 1.3 62.8 + - - +
1206W ILE* 3.2 6.5 + - - +
1207W HIS* 3.1 18.7 + - - +
1220W LEU* 5.8 7.6 - - + -
1251W LEU* 5.8 5.8 - - + -
1255W TYR* 6.2 3.1 - - + -
1261W PHE* 5.0 13.9 - - + +
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Residues in contact with ALA1204 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153W ILE* 6.2 3.6 - - + -
1200W GLU 2.9 12.0 + - - +
1201W CYS* 3.6 9.4 - - - +
1203W LEU* 1.3 76.8 - - - +
1205W ILE* 1.3 63.6 + - - +
1207W HIS* 2.9 25.8 - - - +
1208W CYS* 3.2 5.7 + - - +
1254W ILE* 5.3 14.1 - - + -
1255W TYR* 6.0 3.4 - - - -
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Residues in contact with ILE1205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153W ILE* 6.0 8.1 - - + -
1185W ILE* 5.7 10.5 - - + +
1188W LEU* 6.0 4.3 - - + -
1189W TYR* 5.4 13.5 - - + +
1201W CYS 2.8 11.9 + - - +
1202W LYS* 3.4 11.9 - - - +
1204W ALA* 1.3 77.3 - - - +
1206W ILE* 1.3 63.2 + - + +
1208W CYS* 3.0 10.8 + - - +
1209W ALA* 3.0 20.8 + - - +
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Residues in contact with ILE1206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202W LYS 3.0 15.1 + - - +
1203W LEU* 3.2 4.9 + - - +
1205W ILE* 1.3 75.8 - - - +
1207W HIS* 1.4 51.1 + - - +
1209W ALA* 3.5 7.1 - - + -
1210W GLY 2.6 29.3 + - - -
1211W TYR* 3.0 33.1 + - + +
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Residues in contact with HIS1207 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203W LEU 3.1 9.6 + - - +
1204W ALA* 2.9 20.7 + - - +
1206W ILE* 1.4 75.0 - - - +
1208W CYS* 1.3 56.5 + - - +
1210W GLY* 2.8 21.3 + - - -
1254W ILE 5.7 2.0 - - - +
1255W TYR* 5.0 18.6 - - + -
1258W THR* 6.6 0.2 - - - -
1261W PHE* 5.4 8.4 - - + +
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Residues in contact with CYS1208 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149W GLU* 5.2 13.9 - - + -
1150W VAL* 6.5 0.2 - - - -
1204W ALA 3.2 4.2 + - - +
1205W ILE* 3.0 11.2 + - - +
1207W HIS* 1.3 79.9 - - - +
1209W ALA* 1.3 65.0 + - - +
1210W GLY* 3.2 1.0 + - - -
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Residues in contact with ALA1209 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185W ILE* 5.7 9.0 - - + -
1205W ILE 3.0 12.3 + - - +
1206W ILE* 3.5 13.2 - - + +
1208W CYS* 1.3 77.8 - - - +
1210W GLY* 1.3 62.7 + - - +
1211W TYR* 4.1 9.6 - - + +
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Residues in contact with GLY1210 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206W ILE 2.6 9.6 + - - -
1207W HIS* 2.8 15.3 + - - -
1208W CYS 4.1 0.9 - - - -
1209W ALA* 1.3 81.0 - - - +
1211W TYR* 1.4 61.5 + - - -
1212W SER* 3.3 5.9 + - - -
1260W ARG* 6.3 0.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il